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Center for Computational Systems Medicine
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Protein Summary

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AS Summary

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Protein Functional Features

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Gene Isoform Structures and Expression Levels

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Protein Structures

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pLDDT Score Distribution

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Ramachandran Plot of Protein Structures

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Potential Active Site Information

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Protein Structure and Feature Comparision

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Protein-Protein Interaction

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Related Drugs

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Related Diseases

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Clinically Important Variants

Protein:NFYC

Protein Summary

check button Gene summary
Gene name: NFYC
ASpdb.0 ID: 4802
Gene
Gene symbol

NFYC

Gene ID

4802

Gene namenuclear transcription factor Y subunit gamma
SynonymsCBF-C|CBFC|H1TF2A|HAP5|HSM|NF-YC
Cytomap

1p34.2

Type of geneprotein-coding
Descriptionnuclear transcription factor Y subunit gammaCAAT box DNA-binding protein subunit CCCAAT binding factor subunit CCCAAT transcription binding factor subunit gammahistone H1 transcription factor large subunit 2Anuclear transcription factor Y subunit Cn
Modification date20240305
UniProtAcc

Q13952


check button Gene ontology of this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
GeneNFYC

GO:0000976

transcription cis-regulatory region binding

11256944

GeneNFYC

GO:0000978

RNA polymerase II cis-regulatory region sequence-specific DNA binding

11256944

GeneNFYC

GO:0003677

DNA binding

15243141

GeneNFYC

GO:0005634

nucleus

15243141|15964792

GeneNFYC

GO:0005654

nucleoplasm

-

GeneNFYC

GO:0006355

regulation of DNA-templated transcription

15243141

GeneNFYC

GO:0016602

CCAAT-binding factor complex

15243141

GeneNFYC

GO:0032993

protein-DNA complex

11256944

GeneNFYC

GO:0045944

positive regulation of transcription by RNA polymerase II

23332751

GeneNFYC

GO:0090575

RNA polymerase II transcription regulator complex

11256944



AS Summary

check button Information of the canonical protein with experimentally identified structure from PDB (2023).
UniProt AccFile namePDB IDMethodResolutionChainStartEnd
Q13952-1Q13952-1_6qmq_C.pdb6QMQX-ray2.5C36119

check button ASpdb's canonical and alternatively spliced isoform information.
accession_idgene_namecanonical_idalternative_idcanonical_lengthalternative_lengthcanonical_startcanonical_endtypeoriginalSEQvariationSEQalternative_startalternative_end
Q13952NFYCQ13952-1Q13952-2458335277295Deletionnonenone276276
Q13952NFYCQ13952-1Q13952-2458335316419Deletionnonenone296296
Q13952NFYCQ13952-1Q13952-3458439277295Deletionnonenone276276
Q13952NFYCQ13952-1Q13952-44582976097Deletionnonenone5959
Q13952NFYCQ13952-1Q13952-4458297277295Deletionnonenone238238
Q13952NFYCQ13952-1Q13952-4458297316419Deletionnonenone258258
Q13952NFYCQ13952-1Q13952-5458354316419Deletionnonenone315315
Q13952NFYCQ13952-1Q13952-6458301186219Deletionnonenone185185
Q13952NFYCQ13952-1Q13952-6458301277295Deletionnonenone242242
Q13952NFYCQ13952-1Q13952-6458301316419Deletionnonenone262262
Q13952NFYCQ13952-1Q13952-7458334277295Deletionnonenone276276
Q13952NFYCQ13952-1Q13952-7458334315315Deletionnonenone295295
Q13952NFYCQ13952-1Q13952-7458334316419Deletionnonenone295295

check buttonMultiple sequence alignment of our canonical and alternatively spliced NFYC

check button Matched gene isoform IDs with Ensembl and RefSeq of our canonical and alternative spliced genes of NFYC
UniProt-idENSGENSTENSP
Q13952-1ENSG00000066136.21ENST00000308733.9ENSP00000312617.5
Q13952-2ENSG00000066136.21ENST00000372651.5ENSP00000361734.1
Q13952-2ENSG00000066136.21ENST00000372654.5ENSP00000361738.1
Q13952-2ENSG00000066136.21ENST00000440226.7ENSP00000414299.2
Q13952-2ENSG00000066136.21ENST00000447388.8ENSP00000404427.3
Q13952-3ENSG00000066136.21ENST00000372652.5ENSP00000361736.1
Q13952-4ENSG00000066136.21ENST00000427410.6ENSP00000408315.2
Q13952-5ENSG00000066136.21ENST00000425457.6ENSP00000396620.2
Q13952-6ENSG00000066136.21ENST00000372653.5ENSP00000361737.1
Q13952-7ENSG00000066136.21ENST00000456393.6ENSP00000408867.2

UniProt-idNM IDNP ID
Q13952-1NM_001308114.1NP_001295043.1
Q13952-1XM_017001365.1XP_016856854.1
Q13952-2NM_014223.4NP_055038.2
Q13952-2XM_017001369.1XP_016856858.1
Q13952-3NM_001308115.1NP_001295044.1
Q13952-3XM_006710661.1XP_006710724.1
Q13952-4NM_001142589.1NP_001136061.1
Q13952-5NM_001142588.1NP_001136060.1
Q13952-5XM_006710660.2XP_006710723.2
Q13952-6NM_001142590.1NP_001136062.1
Q13952-7NM_001142587.1NP_001136059.1

check buttonAmino acid sequences of our canonical and alternatively spliced NFYC
accession_idProtein sequence
Q13952-1MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTED
NKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIII
AQPQQGQTTPVTMQVGEGQQVQIVQAQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTL
ATNAQQGQRNASQGKPRRCLKETLQITQTEVQQGQQQFSQFTDGQRNSVQQARVSELTGEAEPREVKATGNSTPCTSSLPTTHPPSHRAG
ASCVCCSQPQQSSTSPPPSDALQWVVVEVSGTPNQLETHRELHAPLPGMTSLSPLHPSQQLYQIQQVTMPAGQDLAQPMFIQSANQPSDG
Q13952-2MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTED
NKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIII
AQPQQGQTTPVTMQVGEGQQVQIVQAQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTL
Q13952-3MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTED
NKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIII
AQPQQGQTTPVTMQVGEGQQVQIVQAQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTL
ATNAQQITQTEVQQGQQQFSQFTDGQRNSVQQARVSELTGEAEPREVKATGNSTPCTSSLPTTHPPSHRAGASCVCCSQPQQSSTSPPPS
Q13952-4MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKRNDIAMAITKFDQFDFLIDIVPRDELKPPKR
QEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIIIAQPQQGQTTPVTMQVGEGQQVQIVQAQPQGQAQQAQSG
TGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQITQTEVQQGQQQFSQFTDGQQLYQIQQVTMPA
Q13952-5MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTED
NKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIII
AQPQQGQTTPVTMQVGEGQQVQIVQAQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTL
Q13952-6MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTED
NKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIII
AQPQQGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTLATNAQQITQTEVQQGQQQFSQFTDGQQLYQIQQV
Q13952-7MSTEGGFGGTSSSDAQQSLQSFWPRVMEEIRNLTVKDFRVQELPLARIKKIMKLDEDVKMISAEAPVLFAKAAQIFITELTLRAWIHTED
NKRRTLQRNDIAMAITKFDQFDFLIDIVPRDELKPPKRQEEVRQSVTPAEPVQYYFTLAQQPTAVQVQGQQQGQQTTSSTTTIQPGQIII
AQPQQGQTTPVTMQVGEGQQVQIVQAQPQGQAQQAQSGTGQTMQVMQQIITNTGEIQQIPVQLNAGQLQYIRLAQPVSGTQVVQGQIQTL

Protein Functional Features

check buttonMain function of this protein. (from UniProt)
NFYC (go to UniProt):Q13952

check buttonRetention analysis result of protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page

* Minus value of BPloci means that the break pointn is located before the CDS.
- Retained protein feature among the 13 regional features.
Accession_idSubsectionStartEndFuncitonal featureSplicing information
Q13952Region305379Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Region305379Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Region305379Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Region305379Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Region305379Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=315;End=315
Q13952Region305379Note=Disordered;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias305325Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias305325Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias305325Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias305325Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias305325Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=315;End=315
Q13952Compositional bias305325Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias339355Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias339355Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias339355Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias339355Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias339355Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias363379Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias363379Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias363379Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias363379Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419
Q13952Compositional bias363379Note=Polar residues;Ontology_term=ECO:0000256;evidence=ECO:0000256|SAM:MobiDB-liteType=Deletion;Start=316;End=419


Gene Isoform Structures and Expression Levels for NFYC

check buttonGene structures of our canonical and alternative spliced genes of NFYC
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
gene isoform structure of NFYC

check button Expression levels of gene isoforms across GTEx.
gtex expression

check button Expression levels of gene isoforms across TCGA.
tcga expression


Protein Structures

check button PDB and CIF files of the predicted protein structures
* Here we show the 3D structure of the proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
3D view using mol* of Q13952-1
3D view using mol* of Q13952-2
3D view using mol* of Q13952-3
3D view using mol* of Q13952-4
3D view using mol* of Q13952-5
3D view using mol* of Q13952-6
3D view using mol* of Q13952-7


pLDDT Score Distribution

check button pLDDT score distribution of the predicted protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
pLDDT distribution across the protein length of Q13952-1
all structure
pLDDT distribution across the protein length of Q13952-2
all structure
pLDDT distribution across the protein length of Q13952-3
all structure
pLDDT distribution across the protein length of Q13952-4
all structure
pLDDT distribution across the protein length of Q13952-5
all structure
pLDDT distribution across the protein length of Q13952-6
all structure
pLDDT distribution across the protein length of Q13952-7
all structure


Ramachandran Plot of Protein Structures


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this protein peptide.
Ramachandran plot of Q13952-1
all structure
Ramachandran plot of Q13952-5
all structure
Ramachandran plot of Q13952-6
all structure

Potential Active Site Information


check button The potential binding sites of these proteins were identified using SiteMap, a module of the Schrodinger suite.
UniProt-idSite scoreSizeD scoreVolumeExposureEnclosureContactPhobicPhilicBalanceDon/AccResidues
Q13952-10.9881491.029311.1010.5420.6430.9080.6290.9110.6910.942380,381,382,383,384,385,386,387,388,389,390,391,41
9,420,421,422,423,424,425,426,427,428,429
Q13952-20.9851081.033340.5990.6280.6240.8680.5910.8630.6850.806191,193,203,250,251,252,253,254,255,256,257,261,26
2,263,264,265,266,267,268,299,300,301,302
Q13952-30.9691500.994445.2140.5990.6470.9340.4911.0240.4790.925192,193,198,199,200,201,202,203,204,205,206,222,22
3,224,225,226,227,228,229,230,238,240,241,243,248,
249,251,252,254,255
Q13952-40.764440.742154.6930.630.6580.8740.750.8480.8840.538187,189,203,205,209,212,213,227,228,229,230,231
Q13952-50.9911151.028426.3490.6110.6510.8520.5620.9280.6060.472173,174,175,176,177,178,179,180,181,188,189,190,19
1,192,193,194,200,203,204,205,223,251,252,255
Q13952-60.909680.896195.1670.5140.741.0640.6920.9920.6970.512171,172,173,174,175,176,177,223,224,226,227,229,24
7,249,251,252,254,269,271
Q13952-71.0672511.125872.5920.4910.7120.941.20.7431.6160.783180,182,191,193,195,201,203,205,225,243,246,247,25
0,251,252,253,254,256,265,266,267,268,269,270,271,
272,273,274,275,276,277,289,291,293,298,300,302,31
7

Protein Structure and Feature Comparision


check button Protein Structure Comparision Using Template Modeling Scores (TM-score).
all structure

check button Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Canonical validated structure (PDB)(green)
3D view using mol* of Q13952-1_Q13952-1_6qmq_C.pdb

check button Protein Structure Comparision Visualization with mol*. between Canonical validated structure (PDB)(orange) vs Alternative predicted structure (AF2)(green)
3D view using mol* of Q13952-1_6qmq_C_Q13952-2.pdb
3D view using mol* of Q13952-1_6qmq_C_Q13952-3.pdb
3D view using mol* of Q13952-1_6qmq_C_Q13952-4.pdb
3D view using mol* of Q13952-1_6qmq_C_Q13952-5.pdb
3D view using mol* of Q13952-1_6qmq_C_Q13952-6.pdb
3D view using mol* of Q13952-1_6qmq_C_Q13952-7.pdb

check button Protein Structure Comparision Visualization with mol*. between Canonical predicted structure (AF2)(orange) vs Alternative predicted structure (AF2)(green)
3D view using mol* of Q13952-1_Q13952-2.pdb
3D view using mol* of Q13952-1_Q13952-3.pdb
3D view using mol* of Q13952-1_Q13952-4.pdb
3D view using mol* of Q13952-1_Q13952-5.pdb
3D view using mol* of Q13952-1_Q13952-6.pdb
3D view using mol* of Q13952-1_Q13952-7.pdb

check button Protein Feature Comparison of the protein sequendary structures among the protiens.
./stats/secondary_structure/figure/Q13952-1_vs_Q13952-2.png
all structure<
./stats/secondary_structure/figure/Q13952-1_vs_Q13952-3.png
all structure<
./stats/secondary_structure/figure/Q13952-1_vs_Q13952-4.png
all structure<
./stats/secondary_structure/figure/Q13952-1_vs_Q13952-5.png
all structure<
./stats/secondary_structure/figure/Q13952-1_vs_Q13952-6.png
all structure<
./stats/secondary_structure/figure/Q13952-1_vs_Q13952-7.png
all structure<

check button Protein Feature Comparison of the relative accessible surface area (ASA) among the protiens.
./stats/relative_asa/Q13952-1_vs_Q13952-2.png
all structure<
./stats/relative_asa/Q13952-1_vs_Q13952-3.png
all structure<
./stats/relative_asa/Q13952-1_vs_Q13952-4.png
all structure<
./stats/relative_asa/Q13952-1_vs_Q13952-5.png
all structure<
./stats/relative_asa/Q13952-1_vs_Q13952-6.png
all structure<
./stats/relative_asa/Q13952-1_vs_Q13952-7.png
all structure<


Protein-Protein Interaction


check button Interactors from UniProt.
Accession_idSubsectionStartEndFuncitonal featureSplicing information


check button Interactors from STRING.
Gene nameInteractors


Related Drugs to NFYC


check button Drugs targeting this gene/protein.
(DrugBank)
UniProt accessionGene nameDrugBank IDDrug nameDrug groupActions

Related Diseases to NFYC


check button Previous studies relating to the alternative splicing of NFYC and disease information from the MeSH term (PubMed)
GenePMIDTitleAbstractMeSH IDMeSH term


Clinically important variants in NFYC


check button (ClinVar, 04/20/2024)
accession_iduniprot_idgene_nameTypeVariantClinical_significance